rune choices:
-MPen reds (almost mandatory)
-Mana regen per level OR Ability Power per level yellows
-Flat magic resistance OR Ability Power per level blues
-Quints are situational depending on the champ, but Flat AP and MS Quints are top choices.

Masteries:
21/9/0 or 21/0/9
21 in Offense, taking all the AP boosting masteries. However, take Brutal Force (+3 Attack Damage) for easier last hitting, this might change if you're playing champs that use abilities to last hit/farm (e.g. karthus). Even if you are a mage, don't forget that your auto attack is essentially free of charge and occasional poke/harass using your auto attacks are very rewarding in times.

9 Defense, suitable if you are playing manaless champions (morde, vlad, rumble). In addition, it works if you're playing a champ who needs to get in close, so you might want that extra durability.

9 Utility, if you have good positioning skills, or if you don't have to get in close to deal damage. Manaless champs can still take 9 Utility by investing in Good Hands, Swiftness and Transmutation.

This is standard for most AP mid lane champs and might change depending on the champ, enemy lane (if you're playing draft and will know who the enemy laner is), whether you want to jungle, etc etc.

If you're playing casual or want to go AP bot or top, the setup might change (for example, picking up Flat Armor yellows for top lane against AD bruisers)